Contacts of the helix formed by residues 471 - 486 (chain D) in PDB entry 1DGH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 471 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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409A PHE* 3.5 16.0 - - - -
5B ARG* 3.4 16.0 - - - +
10B ASP* 5.4 0.4 - - - -
13B GLN* 2.9 41.9 + - - +
180D ASP* 2.9 31.3 + - - +
470D ALA* 1.3 76.5 - - - +
472D ILE* 1.3 66.8 + - - +
473D PHE* 3.8 26.0 - - + -
474D ILE* 3.0 5.7 + - + +
475D GLN* 3.0 18.8 + - - +
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Residues in contact with ILE 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471D GLN* 1.3 74.3 - - - +
473D PHE* 1.3 63.2 + - - +
475D GLN* 3.1 18.4 + - - +
476D LYS* 3.0 46.0 + - + +
501D ASN* 3.7 27.6 - - + +
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Residues in contact with PHE 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A SER* 3.7 35.9 - - - -
409A PHE* 4.0 13.2 - + - -
13B GLN* 4.7 4.3 - - - -
16B LYS* 4.8 7.4 - - - -
184D ASP* 4.7 0.7 - - - -
471D GLN* 3.3 36.7 - - + +
472D ILE* 1.3 78.7 - - - +
474D ILE* 1.3 87.4 + - + +
476D LYS* 3.5 6.7 + - - +
477D LYS* 3.2 23.9 + - + +
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Residues in contact with ILE 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A PHE* 4.1 2.5 - - + -
180D ASP* 3.4 47.8 - - + +
183D TRP* 3.5 42.6 - - + +
184D ASP* 3.9 11.9 - - + +
187D SER* 4.2 2.5 - - - +
467D LEU* 4.8 0.4 - - + -
470D ALA* 4.1 7.2 - - + -
471D GLN 3.0 9.3 + - - +
473D PHE* 1.3 108.0 - - + +
475D GLN* 1.3 66.3 + - - +
477D LYS* 3.5 4.9 + - - +
478D ALA* 3.0 22.9 + - - +
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Residues in contact with GLN 475 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D LEU* 3.8 27.5 - - + +
468D LYS* 3.3 17.0 - - - +
470D ALA 3.0 19.1 - - - +
471D GLN 3.0 16.1 + - - +
472D ILE* 3.1 22.3 + - + +
474D ILE* 1.3 77.2 - - - +
476D LYS* 1.3 59.8 + - + +
478D ALA* 3.3 3.1 + - - +
479D VAL* 2.9 35.1 + - - +
494D GLN* 4.9 5.6 - - - +
497D LEU* 3.8 27.8 - - + +
501D ASN* 3.2 28.4 + - - +
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Residues in contact with LYS 476 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472D ILE* 3.0 37.1 + - + +
473D PHE* 3.8 7.4 - - - +
475D GLN* 1.3 80.0 - - - +
477D LYS* 1.3 57.7 + - - +
479D VAL* 3.2 5.2 + - + +
480D LYS* 2.8 30.4 + - - +
494D GLN* 3.6 33.0 - - - +
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Residues in contact with LYS 477 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D SER* 3.8 35.9 + - - +
188D LEU* 4.4 19.1 + - + +
190D PRO* 6.0 1.8 - - - +
473D PHE* 3.2 16.2 + - + +
474D ILE* 3.8 5.6 - - - +
476D LYS* 1.3 77.2 - - - +
478D ALA* 1.3 63.3 + - - +
480D LYS* 3.4 35.8 + - - +
481D ASN* 3.2 27.5 + - - -
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Residues in contact with ALA 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D TRP* 4.1 27.4 - - + +
187D SER* 3.8 12.9 - - - +
467D LEU* 4.2 14.6 - - + -
474D ILE 3.0 18.3 + - - +
475D GLN 3.6 4.3 - - - +
477D LYS* 1.3 75.2 - - - +
479D VAL* 1.3 63.4 + - - +
481D ASN* 3.0 10.2 + - - +
482D PHE* 3.0 31.7 + - + -
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Residues in contact with VAL 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D LEU* 5.0 2.0 - - + -
475D GLN 2.9 21.2 + - - +
476D LYS* 3.6 4.7 - - + +
478D ALA* 1.3 72.1 - - - +
480D LYS* 1.3 62.6 + - - +
482D PHE* 3.1 8.1 + - - +
483D THR* 2.8 42.4 + - - +
490D GLY 3.7 20.2 - - - +
493D ILE* 4.3 13.5 - - + -
494D GLN* 3.6 31.9 - - + +
497D LEU* 3.8 21.1 - - + -
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Residues in contact with LYS 480 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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476D LYS 2.8 13.3 + - - +
477D LYS* 3.5 40.6 - - - +
478D ALA 3.2 0.2 - - - -
479D VAL* 1.3 77.5 - - - +
481D ASN* 1.3 69.0 + - - +
483D THR* 3.3 8.6 + - - -
484D GLU* 3.2 45.4 + - + +
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Residues in contact with ASN 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D TRP 4.1 2.2 + - - -
187D SER* 2.9 41.4 + - - +
190D PRO* 4.0 21.5 - - - +
193D LEU* 3.9 23.4 - - + +
477D LYS* 3.2 15.5 + - - +
478D ALA* 3.0 9.8 + - - +
480D LYS* 1.3 92.7 + - - +
482D PHE* 1.3 62.5 + - - +
484D GLU* 3.2 22.3 + - - +
485D VAL* 3.5 14.0 + - - +
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Residues in contact with PHE 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D TRP* 3.8 35.4 - + - -
193D LEU* 3.8 21.3 - - + -
196D VAL* 4.4 10.1 - - + -
197D SER* 5.0 1.1 - - - -
463D ILE* 4.1 16.4 - - + -
467D LEU* 4.7 2.9 - - + -
478D ALA* 3.0 34.7 + - + -
479D VAL* 3.1 9.2 + - + +
481D ASN* 1.3 75.5 - - + +
483D THR* 1.3 64.0 + - - +
485D VAL* 3.0 17.5 + - - +
486D HIS 3.1 12.0 + - - +
489D TYR* 3.5 40.7 - + + +
490D GLY* 3.8 18.8 - - - +
493D ILE* 3.6 20.2 - - + -
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Residues in contact with THR 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479D VAL* 2.8 30.1 + - - +
480D LYS* 3.5 9.5 - - - -
481D ASN 3.3 0.2 - - - -
482D PHE* 1.3 72.6 - - - +
484D GLU* 1.3 61.7 + - + +
486D HIS* 3.2 22.9 - - - -
487D PRO* 3.3 20.4 - - + +
490D GLY* 3.5 15.9 - - - -
491D SER 4.5 0.7 + - - -
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Residues in contact with GLU 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D PRO* 6.0 2.1 - - - +
193D LEU* 5.9 0.5 - - - +
440D VAL* 4.2 21.4 - - + +
444D ARG* 3.1 19.2 + - - -
480D LYS* 3.2 46.0 + - + +
481D ASN* 3.5 16.1 - - - +
482D PHE 3.2 0.8 - - - -
483D THR* 1.3 73.7 - - + +
485D VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D LEU* 3.6 27.4 - - + -
440D VAL* 3.9 12.6 - - + +
443D VAL* 3.7 22.0 - - + +
444D ARG* 2.9 64.5 + - - +
447D TYR* 4.7 1.8 - - + -
481D ASN 3.6 13.7 - - - +
482D PHE* 3.0 9.7 + - - +
484D GLU* 1.3 76.9 - - - +
486D HIS* 1.3 61.7 + - + +
489D TYR* 3.8 18.2 - - + -
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Residues in contact with HIS 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444D ARG* 4.5 10.5 - - + +
447D TYR* 4.1 15.3 - + + -
448D VAL* 3.8 25.3 - - + +
482D PHE 3.1 4.7 + - - +
483D THR 3.2 5.0 + - - +
485D VAL* 1.3 82.0 - - + +
487D PRO* 1.3 72.7 - - + +
488D ASP* 2.9 46.9 + - + +
489D TYR* 2.8 37.5 + - + +
490D GLY 3.2 4.5 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il